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Nonsense-mediated mRNA Decay

Nonsense-mediated mRNA Decay

The Upf proteins that carry out nonsense-mediated decay (NMD) are found in all eukaryotic organisms, including humans. Each protein has an individual role, but they need to work in collaboration. Upf1 is an ATP-dependent RNA helicase that unwinds the RNA helix. Because Upf1 can unwind any RNA, Upf2 and Upf3 are required to help Upf1 discriminate between nonsense and normal mRNAs.
Usually, Upf3 binds to an Exon Junction Complex (EJC) at mRNA splice sites. If a ribosome fully translates the mRNA,...

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Related Experiment Video

Updated: Jun 18, 2025

Differentiation of a Human Neural Stem Cell Line on Three Dimensional Cultures, Analysis of MicroRNA and Putative Target Genes

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NMDtxDB: data-driven identification and annotation of human NMD target transcripts.

Thiago Britto-Borges^1,2, Niels H Gehring^3,4, Volker Boehm^3,4

¹Section of Bioinformatics and Systems Cardiology, Department of Internal Medicine III and Klaus Tschira Institute for Integrative Computational Cardiology, Heidelberg University Hospital, 69120 Heidelberg, Germany.

RNA (New York, N.Y.)

|August 2, 2024

Summary

This summary is machine-generated.

This study introduces a data-driven approach to identify nonsense-mediated RNA decay (NMD) target transcripts. The NMDtxDB database provides a comprehensive resource for studying NMD-sensitive RNAs and their regulation.

Keywords:

alternative splicing computational workflow mRNA decay nonsense-mediated RNA decay premature stop codon

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Last Updated: Jun 18, 2025

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Identification of Alternative Splicing and Polyadenylation in RNA-seq Data

Identification of Alternative Splicing and Polyadenylation in RNA-seq Data

Published on: June 24, 2021

Area of Science:

Molecular Biology
Genomics
Bioinformatics

Background:

The nonsense-mediated RNA decay (NMD) pathway is essential for mRNA quality control.
Current NMD substrate RNA annotations rely on general rules rather than empirical data.

Purpose of the Study:

To develop a data-driven workflow for identifying NMD target transcripts.
To create a comprehensive database (NMDtxDB) of NMD-sensitive transcripts.

Main Methods:

Utilized Nanopore and Illumina sequencing for transcriptome assembly.
Integrated coding sequence information from Ensembl, Gencode, and OpenProt for enhanced annotation.
Performed knockdowns/knockout of SMG5, SMG6, and SMG7 genes in four cell lines.

Main Results:

Assembled 302,889 transcripts, with 24% not present in Ensembl annotations.
Identified 48,213 transcripts containing premature stop codons.
Found 6433 transcripts significantly upregulated in NMD-deficient versus NMD-active cells.

Conclusions:

The NMDtxDB database offers an in-depth view of NMD-sensitive transcripts.
The study provides an open-source analysis workflow and web application for NMD research.
This work enhances the understanding and annotation of NMD targets.